Preheat oven to 375°F. Spray a 9x13 baking dish with cooking spray. Set aside.
In a large skillet on medium-high heat, add the lean ground beef, diced yellow onion, salt, and black pepper. Cook, and brown the ground beef until no pink remains. Drain any excess fat from the skillet.
Add taco seasoning, water, green chilis, and seasoned black beans to the skillet of cooked ground beef. Stir to coat all the beef in the taco seasoning. Turn the heat down to medium and allow the meat mixture to cook for an additional 2-3 minutes or until most of the moisture has evaporated. Remove from heat.
Place 2 flour tortillas into the bottom of the sprayed 9x13 baking dish. The tortillas will overlap slightly in the center.
Spread ⅓ of the meat mixture evenly over the flour tortillas. Top with ½ cup salsa spread over the meat mixture. Sprinkle ½ cup of the shredded cheddar cheese and ½ cup of the Monterey jack cheese evenly over the meat and salsa.
Place 4 flour tortillas (2 on top of each other) as the next layer in the baking dish, followed by another ⅓ of the meat mixture, ½ cup salsa, ½ cup shredded cheddar cheese, and ½ cup shredded Monterey jack cheese.
Add the last layer of 4 flour tortillas (2 on top of each other), the final ⅓ of the meat mixture, ½ cup salsa, and the remaining shredded cheddar and Monterey jack cheese.
Bake the Mexican lasagna in the center rack of the oven for 30-35 minutes or until the cheese is melted, bubbly, and lightly browned.
Allow the Mexican lasagna to cool on the counter for 15 minutes before garnishing it with chopped cilantro. You can add an optional garnish to individual servings of a dollop of sour cream and a sprinkle of diced tomatoes.
Be sure to buy blocks of cheese and shred them yourself. Pre-shredded cheese has a coating on it which can impact how it melts.
We doubled up on the center and top layers of the flour tortillas to give them extra structure, as the flour tortillas tend to get very soft when they absorb the liquids when baked.
You can swap out the larger flour tortillas for the smaller-sized ones if that is what you have on hand. You just need to note that you will need to use more tortillas for each layer if using the smaller ones.
Oven temperatures vary and may need to be recalibrated periodically to ensure they are accurate. Make sure to check your lasagna at the lower end of the recommended baking time.